Use of Genomic Resources to Assess Adaptive Divergence and Introgression in Oaks

Adaptive divergence is widely accepted as a contributor to speciation and the maintenance of species integrity. However, the mechanisms leading to reproductive isolation, the genes involved in adaptive divergence, and the traits that shape the adaptation of wild species to changes in climate are still largely unknown. In studying the role of ecological interactions and environment-driven selection, trees have emerged as potential model organisms because of their longevity and large genetic diversity, especially in natural habitats. Due to recurrent gene flow among species with different ecological preferences, oaks arose as early as the 1970s as a model for understanding how speciation can occur in the face of interspecific gene flow, and what we mean by “species” when geographically and genomically heterogeneous introgression seems to undermine species’ genetic coherence. In this review, we provide an overview of recent research into the genomic underpinnings of adaptive divergence and maintenance of species integrity in oaks in the face of gene flow. We review genomic and analytical tools instrumental to better understanding mechanisms leading to reproductive isolation and environment-driven adaptive introgression in oaks. We review evidence that oak species are genomically coherent entities, focusing on sympatric populations with ongoing gene flow, and discuss evidence for and hypotheses regarding genetic mechanisms linking adaptive divergence and reproductive isolation. As the evolution of drought- and freezing-tolerance have been key to the parallel diversification of oaks, we investigate the question of whether the same or a similar set of genes are involved in adaptive divergence for drought and stress tolerance across different taxa and sections. Finally, we propose potential future research directions on the role of hybridization and adaptive introgression in adaptation to climate change.

Molecular Signatures of Reticulate Evolution within the Complex of European Pine Taxa

Speciation mechanisms, including the role of interspecific gene flow and introgression in the emergence of new species, are the major focus of evolutionary studies. Inference of taxonomic relationship between closely related species may be challenged by past hybridization events, but at the same time, it may provide new knowledge about mechanisms responsible for the maintenance of species integrity despite interspecific gene flow. Here, using nucleotide sequence variation and utilizing a coalescent modeling framework, we tested the role of hybridization and introgression in the evolutionary history of closely related pine taxa from the Pinus mugo complex and P. sylvestris. We compared the patterns of polymorphism and divergence between taxa and found a great overlap of neutral variation within the P. mugo complex. Our phylogeny reconstruction indicated multiple instances of reticulation events in the past, suggesting an important role of interspecific gene flow in the species divergence. The best-fitting model revealed P. mugo and P. uncinata as sister species with basal P. uliginosa and asymmetric migration between all investigated species after their divergence. The magnitude of interspecies gene flow differed greatly, and it was consistently stronger from representatives of P. mugo complex to P. sylvestris than in the opposite direction. The results indicate the prominent role of reticulation evolution in those forest trees and provide a genetic framework to study species integrity maintained by selection and local adaptation.

Dinophyceae use exudates as weapons against the parasite Amoebophrya sp. (Syndiniales)

SummaryParasites of the genus Amoebophrya sp. are important contributors to marine ecosystems and can be determining factors in the demise of blooms of Dinophyceae, including microalgae commonly responsible for toxic red tides. Yet they rarely lead to the total collapse of Dinophyceae blooms. The addition of resistant Dinophyceae (Alexandrium minutum or Scrippsiella donghaienis) or their exudate into a well-established host-parasite culture (Scrippsiella acuminata-Amoebophrya sp.) mitigated the success of the parasite and increased the survival of the sensitive host. Effect were mediated via water-borne molecules without the need of a physical contact. Severity of the anti-parasitic defenses fluctuated depending on the species, the strain and its concentration, but never totally prevented the parasite transmission. The survival time of Amoebophrya sp. free-living stages (dinospores) decreased in presence of A. minutum but not of S. donghaienis. The progeny drastically decreased with both species. Integrity of the membrane of dinospores was altered by A. minutum which provided a first indication on the mode of action of these anti-parasitic molecules. These results demonstrate that extracellular defenses are an effective strategy against parasites that does not only protect the resistant cells but also have the potential to affect the whole surrounding community.

Neutral and adaptive genomic variation in hybrid zones of two ecologically diverged Petunia species (Solanaceae)

Hybridization between closely related plant species is a widespread phenomenon with significant evolutionary consequences, so natural hybrid zones provide exciting opportunities to study the processes of genetic differentiation and species formation. In Petunia, genetics, ecology and evolution of pollination syndromes have been thoroughly studied and related to the development of prezygotic isolation barriers between species. However, to date, no studies have explored the importance of extrinsic post-zygotic barriers such as environmental selection as drivers of reproductive isolation. In this study, we applied a population genetics approach to understand the speciation of two partially sympatric taxa of Petunia Juss that hybridize in the wild despite having strong differences in pollination syndrome, mating system and environmental requirements. We evaluated 58 individuals from seven allopatric and two contact zones of Petunia axillaris and P. exserta with genomic data to study the population genetic structure and gene exchange between these species and scan for potential loci under natural selection related to the preservation of species barriers. We explicitly evaluated the time, intensity and direction of interspecific migration, testing for alternative demographic scenarios. The genetic structure showed well-differentiated species-level lineages, and poor differentiation among populations of P. axillaris; P. exserta populations were highly structured, with several well-differentiated intraspecific lineages. Our data provide evidence for admixture with low asymmetric gene flow from P. axillaris to P. exserta associated with recent secondary contact, suggesting that pollinator specificity is not the only trait responsible for species integrity in this system. Combining the results from FST outlier and genotype–phenotype association methods, we identified 54 non-synonymous candidate variants under natural selection. Those variants are found in 35 coding sequences from which we found genes related to light-response networks, supporting that extrinsic factors such as habitat preferences can also provide a mechanism of reproductive isolation between Petunia spp. We argue that a set of pre- and post-zygotic barriers in conjunction with demographic processes maintain the species integrity.

The Preferred Account of Human Capabilities

Chapter 3 translates the idea of dignity as species integrity into the more grounded idea of respecting central human capabilities. Fleshing out human capabilities yields a preferred capability list, which is balanced, life stage sensitive, and provisional. This conception of human dignity carries the advantage of avoiding speciesism, the view that members of one’s own species are morally superior. It leaves open the possibility that members of nonhuman species possess their own kind of dignity, based on central capabilities for their species. Dignity as species integrity carries the advantage of avoiding ableism. In contrast to Kantian conceptions, which regard highly developed cognitive functioning as necessary for dignity, Chapter 3 equates dignity with possessing at least one central human capability. Infants and people with disabilities who can affiliate, express emotion, or exercise senses and imagination possess a human dignity that demands respect, even if they lack specific cognitive capabilities.

What Matters for Individuals in Later Life?

Chapter 2 introduces the idea of dignity as species integrity. For human beings, respecting dignity requires making reasonable efforts to support human capabilities at a basic floor level. Human capabilities include the central kinds of things we can do and be as human beings, including capacities for a life narrative; health; bodily integrity; senses, imagination, and thought; emotions; practical reason; affiliation; relating to nature; play; and participating in the environment. Contrary to what “healthy aging” advocates claim, medical progress will not eliminate threats to these human capabilities. Chapter 2 compares dignity as species integrity with sub-Saharan African conceptions of Ubuntu, the Nguni word for “humanness.” Ubuntu prizes relational values and human capacities for harmonious relationship. The chapter concludes that to have global traction, capability lists must be balanced, life stage informed, and provisional.

A species-discriminatory single-nucleotide polymorphism set reveals maintenance of species integrity in hybridizing European white oaks (Quercus spp.) despite high levels of admixture

Background and Aims Hybridization and introgression play an important role in the evolution and diversification of plants. To assess the degree of past and current hybridization, the level of genetic admixture in populations needs to be investigated. Ongoing hybridization and blurred species separation have made it challenging to assign European white oak taxa based on leaf morphology and/or genetic markers and to assess the level of admixture. Therefore, there is a need for powerful markers that differentiate between taxa. Here, we established a condensed set of single-nucleotide polymorphism (SNP) markers to reliably differentiate between the three most common oak species in temperate European forests (Quercus robur, Q. petraea, Q. pubescens) and to assess the degree of admixture in a large set of selected Swiss populations. Methods A training set of 194 presumably pure reference samples from Switzerland and Europe was used to assign 633 test individuals with two different approaches (population genetic-based/Bayesian vs. assumption-free/discriminative classifier) using 58 selected SNPs from coding regions. Admixture was calculated at the individual and population level with the Shannon diversity index based on individual assignment probabilities. Key Results Depending on the approach, 97.5–100 % of training individuals were assigned correctly, and additional analyses showed that the established SNP set could be further reduced while maintaining its discriminatory power. The two assignment approaches showed high overlap (99 %) in assigning training individuals and slightly less overlap in test individuals (84 %). Levels of admixture varied widely among populations. Mixed stands of Q. petraea and Q. pubescens revealed much higher degrees of admixture than mixed stands of the other two taxon pairs, accentuating high levels of gene flow between these two taxa in Switzerland. Conclusions Our set of SNPs warrants reliable taxon discrimination with great potential for further applications. We show that the three European white oak taxa have largely retained their species integrity in Switzerland despite high levels of admixture.